Real time PCR has created a revolution in diagnostics, with increased speed, sensitivity and specificity over many other offerings. The components of real time PCR tests can include, e.g., i) master mix (containing enzyme, buffer, and nucleotides), ii) positive controls, iii) internal positive controls (to ensure proper nucleic acid purification), iv) detection mix (containing the target-specific primers and probes), v) internal sample control; or vi) combinations thereof. The instant invention provides PCR systems, including real-time PCR systems, in which all tests and testing protocols are standardized. The goal of this platform is to minimize both handling of material and time spent running samples. For example, a single Internal Positive Control (IPC) can provide a means to ensure proper nucleic acid purification for both RNA and DNA test targets. Additionally, standard cycling conditions for all diagnostic tests allow the user to run both RNA and DNA targets side-by-side on the same reaction plate. The assays will run in approximately one hour, or less. A number of real time PCR tests have been developed on the new platform. Analytical sensitivity analysis for IDEXX RealPCR Mycoplasma gallisepticum, M. synoviae, Bovine Viral Diarrhea Virus (BVDV), Bluetongue Virus (BTV), and Mycobacterium avium subspecies paratuberculosis (MAP) tests each demonstrate sensitivity of ≤10 copies per reaction with high specificity and compatibly for use with one or more internal positive controls and/or internal sample controls. Standardized protocols and components in the test system will provide laboratories a more efficient and flexible platform for PCR testing, including real-time PCR, that will greatly minimize component handling, simplify workflows, reduce the likelihood of operator error, and reduce total testing time.